Thanks Bert, I did understand not to delete such atoms or set occupancy to zero from forum and literature. However, colleagues in the vicinity informed to take approaches i mentioned earlier. Therefore, I thought to take opinion from forum if something has changed recently.
Thanking, On Thu, May 4, 2017 at 8:55 PM, Bert Van-Den-Berg < [email protected]> wrote: > This has been discussed before, I guess more than once.... > > I think most people (I'm sure i'll be corrected if wrong) would favor not > removing any atoms or setting occupancies to zero and let the invisible > atoms be accounted for by high B-factors (either set manually or just > letting refinement do its thing). > > > Bert > > > ------------------------------ > *From:* CCP4 bulletin board <[email protected]> on behalf of Vipul > Panchal <[email protected]> > *Sent:* 04 May 2017 16:12 > *To:* [email protected] > *Subject:* [ccp4bb] Poor density fit. > > HI all. > > I am solving protein structure with 2.16A resolution. There are two chain > in an asymmetric unit. I see that in one of the chain, many residues' > density for side chains is incomplete and therefore results in poor density > fit. > > *I want to know your opinions for the approach I have taken. Figures > relevant to each approach have been attached herewith.* > > *Case1*: There is no experimental density at all. Therefore, i have > deleted side chains to Gly. > *Case2*: Though there is incomplete density for Leu, it is enough to > suggest its rotamer. In this case, as may be seen, i have just set > occupancy for atoms without density(CG, CD1, CD2) to zero. > > Hopeful for the response. > > -- > Vipul Panchal > Senior Research Fellow, > Respiratory disease and biology, > CSIR-IGIB > (M)-9540113372 > -- Vipul Panchal Senior Research Fellow, Respiratory disease and biology, CSIR-IGIB (M)-9540113372
